The invention relates to methods and systems for predicting or estimating the
melting temperature of duplex nucleic acids, particularly duplexes of oligonucleotides
which may be used, for example, as primers or probes in PCR and/or hybridization
assays. The invention also relates to methods and systems for designing and selecting
oligonucleotide probes and primers having a predicted melting temperature which
is optimized for such assays. To this end, algorithms and methods are provided
for predicting the melting temperature of a nucleic acid having a predetermined
sequence. These methods and algorithms estimate the melting temperature of a nucleic
acid duplex under particular salt conditions. The methods and algorithms use novel
formulas, having terms and coefficients that are functions of the particular nucleotide
sequence, to estimate the effect of particular salt conditions on the melting temperature.
As such, the methods and systems of the invention provide superior result compared
to existing methods, which do not consider sequence dependent effects of changing
salt conditions.
